Job ID = 6455444 SRX = SRX287794 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:04:55 prefetch.2.10.7: 1) Downloading 'SRR869983'... 2020-06-21T10:04:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:07:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:07:11 prefetch.2.10.7: 1) 'SRR869983' was downloaded successfully Read 17133552 spots for SRR869983/SRR869983.sra Written 17133552 spots for SRR869983/SRR869983.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:07 17133552 reads; of these: 17133552 (100.00%) were unpaired; of these: 963576 (5.62%) aligned 0 times 11195771 (65.34%) aligned exactly 1 time 4974205 (29.03%) aligned >1 times 94.38% overall alignment rate Time searching: 00:05:08 Overall time: 00:05:08 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 2735079 / 16169976 = 0.1691 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 19:17:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287794/SRX287794.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287794/SRX287794.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287794/SRX287794.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287794/SRX287794.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 19:17:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:17:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:17:26: 1000000 INFO @ Sun, 21 Jun 2020 19:17:32: 2000000 INFO @ Sun, 21 Jun 2020 19:17:37: 3000000 INFO @ Sun, 21 Jun 2020 19:17:43: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 19:17:49: 5000000 INFO @ Sun, 21 Jun 2020 19:17:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287794/SRX287794.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287794/SRX287794.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287794/SRX287794.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287794/SRX287794.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 19:17:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:17:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:17:55: 6000000 INFO @ Sun, 21 Jun 2020 19:17:57: 1000000 INFO @ Sun, 21 Jun 2020 19:18:01: 7000000 INFO @ Sun, 21 Jun 2020 19:18:03: 2000000 INFO @ Sun, 21 Jun 2020 19:18:08: 8000000 INFO @ Sun, 21 Jun 2020 19:18:10: 3000000 INFO @ Sun, 21 Jun 2020 19:18:14: 9000000 INFO @ Sun, 21 Jun 2020 19:18:16: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 19:18:20: 10000000 INFO @ Sun, 21 Jun 2020 19:18:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287794/SRX287794.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287794/SRX287794.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287794/SRX287794.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287794/SRX287794.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 19:18:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:18:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:18:23: 5000000 INFO @ Sun, 21 Jun 2020 19:18:27: 11000000 INFO @ Sun, 21 Jun 2020 19:18:27: 1000000 INFO @ Sun, 21 Jun 2020 19:18:29: 6000000 INFO @ Sun, 21 Jun 2020 19:18:33: 12000000 INFO @ Sun, 21 Jun 2020 19:18:33: 2000000 INFO @ Sun, 21 Jun 2020 19:18:35: 7000000 INFO @ Sun, 21 Jun 2020 19:18:39: 13000000 INFO @ Sun, 21 Jun 2020 19:18:40: 3000000 INFO @ Sun, 21 Jun 2020 19:18:42: 8000000 INFO @ Sun, 21 Jun 2020 19:18:42: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:18:42: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:18:42: #1 total tags in treatment: 13434897 INFO @ Sun, 21 Jun 2020 19:18:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:18:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:18:43: #1 tags after filtering in treatment: 13434897 INFO @ Sun, 21 Jun 2020 19:18:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:18:43: #1 finished! INFO @ Sun, 21 Jun 2020 19:18:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:18:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:18:44: #2 number of paired peaks: 441 WARNING @ Sun, 21 Jun 2020 19:18:44: Fewer paired peaks (441) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 441 pairs to build model! INFO @ Sun, 21 Jun 2020 19:18:44: start model_add_line... INFO @ Sun, 21 Jun 2020 19:18:44: start X-correlation... INFO @ Sun, 21 Jun 2020 19:18:44: end of X-cor INFO @ Sun, 21 Jun 2020 19:18:44: #2 finished! INFO @ Sun, 21 Jun 2020 19:18:44: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 19:18:44: #2 alternative fragment length(s) may be 4,44 bps INFO @ Sun, 21 Jun 2020 19:18:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287794/SRX287794.05_model.r WARNING @ Sun, 21 Jun 2020 19:18:44: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:18:44: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Sun, 21 Jun 2020 19:18:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:18:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:18:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:18:46: 4000000 INFO @ Sun, 21 Jun 2020 19:18:48: 9000000 INFO @ Sun, 21 Jun 2020 19:18:52: 5000000 INFO @ Sun, 21 Jun 2020 19:18:54: 10000000 INFO @ Sun, 21 Jun 2020 19:18:58: 6000000 INFO @ Sun, 21 Jun 2020 19:19:00: 11000000 INFO @ Sun, 21 Jun 2020 19:19:04: 7000000 INFO @ Sun, 21 Jun 2020 19:19:07: 12000000 INFO @ Sun, 21 Jun 2020 19:19:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:19:10: 8000000 INFO @ Sun, 21 Jun 2020 19:19:13: 13000000 INFO @ Sun, 21 Jun 2020 19:19:16: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:19:16: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:19:16: #1 total tags in treatment: 13434897 INFO @ Sun, 21 Jun 2020 19:19:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:19:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:19:16: 9000000 INFO @ Sun, 21 Jun 2020 19:19:16: #1 tags after filtering in treatment: 13434897 INFO @ Sun, 21 Jun 2020 19:19:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:19:16: #1 finished! INFO @ Sun, 21 Jun 2020 19:19:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:19:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:19:17: #2 number of paired peaks: 441 WARNING @ Sun, 21 Jun 2020 19:19:17: Fewer paired peaks (441) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 441 pairs to build model! INFO @ Sun, 21 Jun 2020 19:19:17: start model_add_line... INFO @ Sun, 21 Jun 2020 19:19:17: start X-correlation... INFO @ Sun, 21 Jun 2020 19:19:17: end of X-cor INFO @ Sun, 21 Jun 2020 19:19:17: #2 finished! INFO @ Sun, 21 Jun 2020 19:19:17: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 19:19:17: #2 alternative fragment length(s) may be 4,44 bps INFO @ Sun, 21 Jun 2020 19:19:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287794/SRX287794.10_model.r WARNING @ Sun, 21 Jun 2020 19:19:17: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:19:17: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Sun, 21 Jun 2020 19:19:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:19:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:19:17: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:19:22: 10000000 INFO @ Sun, 21 Jun 2020 19:19:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287794/SRX287794.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:19:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287794/SRX287794.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:19:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287794/SRX287794.05_summits.bed INFO @ Sun, 21 Jun 2020 19:19:22: Done! pass1 - making usageList (615 chroms): 1 millis pass2 - checking and writing primary data (2441 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:19:27: 11000000 INFO @ Sun, 21 Jun 2020 19:19:33: 12000000 INFO @ Sun, 21 Jun 2020 19:19:39: 13000000 INFO @ Sun, 21 Jun 2020 19:19:41: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:19:41: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:19:41: #1 total tags in treatment: 13434897 INFO @ Sun, 21 Jun 2020 19:19:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:19:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:19:42: #1 tags after filtering in treatment: 13434897 INFO @ Sun, 21 Jun 2020 19:19:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:19:42: #1 finished! INFO @ Sun, 21 Jun 2020 19:19:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:19:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:19:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:19:43: #2 number of paired peaks: 441 WARNING @ Sun, 21 Jun 2020 19:19:43: Fewer paired peaks (441) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 441 pairs to build model! INFO @ Sun, 21 Jun 2020 19:19:43: start model_add_line... INFO @ Sun, 21 Jun 2020 19:19:43: start X-correlation... INFO @ Sun, 21 Jun 2020 19:19:43: end of X-cor INFO @ Sun, 21 Jun 2020 19:19:43: #2 finished! INFO @ Sun, 21 Jun 2020 19:19:43: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 19:19:43: #2 alternative fragment length(s) may be 4,44 bps INFO @ Sun, 21 Jun 2020 19:19:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287794/SRX287794.20_model.r WARNING @ Sun, 21 Jun 2020 19:19:43: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:19:43: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Sun, 21 Jun 2020 19:19:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:19:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:19:43: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:19:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287794/SRX287794.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:19:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287794/SRX287794.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:19:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287794/SRX287794.10_summits.bed INFO @ Sun, 21 Jun 2020 19:19:56: Done! pass1 - making usageList (509 chroms): 1 millis pass2 - checking and writing primary data (1741 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:20:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:20:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287794/SRX287794.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:20:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287794/SRX287794.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:20:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287794/SRX287794.20_summits.bed INFO @ Sun, 21 Jun 2020 19:20:21: Done! pass1 - making usageList (286 chroms): 1 millis pass2 - checking and writing primary data (585 records, 4 fields): 8 millis CompletedMACS2peakCalling